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The security ministry placed government buildings on high alert after the Pentagon confirmed Friday that the U.S. operation in Somalia killed Ahmed Godane.
Intelligence reports indicate the group is planning attacks in Somalia, according to Mohamed Yusuf, a spokesman for the national security ministry.
The U.S. military said it killed Godane in a thunderous attack Monday.
"Removing Godane from the battlefield is a major symbolic and operational loss to Al-Shabaab," said Rear Adm. John Kirby, the Pentagon press secretary.
Godane has been at the helm since the group started a campaign of terror in East Africa, killing Somali officials, aid workers and others in a spate of suicide bombings.
U.S. officials were tipped off to what Kirby called "actionable intelligence ... strong enough" to suggest his whereabouts.
Commandos flew in Monday and took the leader out with the help of drones and laser-guided missiles, Kirby said.